Multiple sequence alignment - TraesCS5A01G267400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G267400 chr5A 100.000 2498 0 0 1 2498 478847984 478850481 0.000000e+00 4614.0
1 TraesCS5A01G267400 chr5A 96.914 1458 33 6 1 1447 457097408 457098864 0.000000e+00 2433.0
2 TraesCS5A01G267400 chr5A 98.290 994 17 0 1447 2440 457100821 457101814 0.000000e+00 1742.0
3 TraesCS5A01G267400 chr5B 99.877 2447 2 1 1 2446 529689540 529691986 0.000000e+00 4501.0
4 TraesCS5A01G267400 chr5B 95.082 61 2 1 2439 2498 453876792 453876732 7.360000e-16 95.3
5 TraesCS5A01G267400 chr7B 97.255 1457 29 5 1 1447 505223916 505222461 0.000000e+00 2459.0
6 TraesCS5A01G267400 chr3B 97.186 1457 31 5 1 1447 782216186 782214730 0.000000e+00 2455.0
7 TraesCS5A01G267400 chr7D 96.914 1458 33 6 1 1447 64828340 64826884 0.000000e+00 2433.0
8 TraesCS5A01G267400 chr7D 98.390 994 15 1 1447 2440 64825935 64824943 0.000000e+00 1746.0
9 TraesCS5A01G267400 chr5D 96.914 1458 33 6 1 1447 468181631 468180175 0.000000e+00 2433.0
10 TraesCS5A01G267400 chr5D 98.295 997 16 1 1447 2443 468179469 468178474 0.000000e+00 1746.0
11 TraesCS5A01G267400 chr4D 96.914 1458 33 6 1 1447 505351043 505349587 0.000000e+00 2433.0
12 TraesCS5A01G267400 chr4D 98.390 994 15 1 1447 2440 505348576 505347584 0.000000e+00 1746.0
13 TraesCS5A01G267400 chr4B 96.914 1458 33 6 1 1447 42253580 42255036 0.000000e+00 2433.0
14 TraesCS5A01G267400 chr4B 98.390 994 15 1 1447 2440 42255742 42256734 0.000000e+00 1746.0
15 TraesCS5A01G267400 chr3A 96.916 1459 32 7 1 1447 690942485 690943942 0.000000e+00 2433.0
16 TraesCS5A01G267400 chr3A 98.390 994 15 1 1447 2440 690944657 690945649 0.000000e+00 1746.0
17 TraesCS5A01G267400 chr4A 98.395 997 15 1 1447 2443 27194403 27193408 0.000000e+00 1751.0
18 TraesCS5A01G267400 chr3D 98.390 994 15 1 1447 2440 562175868 562174876 0.000000e+00 1746.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G267400 chr5A 478847984 478850481 2497 False 4614.0 4614 100.0000 1 2498 1 chr5A.!!$F1 2497
1 TraesCS5A01G267400 chr5A 457097408 457101814 4406 False 2087.5 2433 97.6020 1 2440 2 chr5A.!!$F2 2439
2 TraesCS5A01G267400 chr5B 529689540 529691986 2446 False 4501.0 4501 99.8770 1 2446 1 chr5B.!!$F1 2445
3 TraesCS5A01G267400 chr7B 505222461 505223916 1455 True 2459.0 2459 97.2550 1 1447 1 chr7B.!!$R1 1446
4 TraesCS5A01G267400 chr3B 782214730 782216186 1456 True 2455.0 2455 97.1860 1 1447 1 chr3B.!!$R1 1446
5 TraesCS5A01G267400 chr7D 64824943 64828340 3397 True 2089.5 2433 97.6520 1 2440 2 chr7D.!!$R1 2439
6 TraesCS5A01G267400 chr5D 468178474 468181631 3157 True 2089.5 2433 97.6045 1 2443 2 chr5D.!!$R1 2442
7 TraesCS5A01G267400 chr4D 505347584 505351043 3459 True 2089.5 2433 97.6520 1 2440 2 chr4D.!!$R1 2439
8 TraesCS5A01G267400 chr4B 42253580 42256734 3154 False 2089.5 2433 97.6520 1 2440 2 chr4B.!!$F1 2439
9 TraesCS5A01G267400 chr3A 690942485 690945649 3164 False 2089.5 2433 97.6530 1 2440 2 chr3A.!!$F1 2439
10 TraesCS5A01G267400 chr4A 27193408 27194403 995 True 1751.0 1751 98.3950 1447 2443 1 chr4A.!!$R1 996
11 TraesCS5A01G267400 chr3D 562174876 562175868 992 True 1746.0 1746 98.3900 1447 2440 1 chr3D.!!$R1 993

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1138 1157 3.591977 AGGTAAAGGCAGGAAGTATGGTT 59.408 43.478 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2473 5469 0.31812 CAATCAAAGCCGCAAACCCT 59.682 50.0 0.0 0.0 0.0 4.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1138 1157 3.591977 AGGTAAAGGCAGGAAGTATGGTT 59.408 43.478 0.00 0.00 0.00 3.67
2440 5436 1.134175 GGCACAATCCAAACATACCCG 59.866 52.381 0.00 0.00 0.00 5.28
2443 5439 3.630312 GCACAATCCAAACATACCCGTAT 59.370 43.478 0.00 0.00 0.00 3.06
2445 5441 5.732247 GCACAATCCAAACATACCCGTATTC 60.732 44.000 0.00 0.00 0.00 1.75
2446 5442 5.355630 CACAATCCAAACATACCCGTATTCA 59.644 40.000 0.00 0.00 0.00 2.57
2447 5443 5.946972 ACAATCCAAACATACCCGTATTCAA 59.053 36.000 0.00 0.00 0.00 2.69
2448 5444 6.605594 ACAATCCAAACATACCCGTATTCAAT 59.394 34.615 0.00 0.00 0.00 2.57
2449 5445 7.123547 ACAATCCAAACATACCCGTATTCAATT 59.876 33.333 0.00 0.00 0.00 2.32
2450 5446 7.654022 ATCCAAACATACCCGTATTCAATTT 57.346 32.000 0.00 0.00 0.00 1.82
2451 5447 7.090953 TCCAAACATACCCGTATTCAATTTC 57.909 36.000 0.00 0.00 0.00 2.17
2452 5448 5.968848 CCAAACATACCCGTATTCAATTTCG 59.031 40.000 0.00 0.00 0.00 3.46
2453 5449 4.806342 ACATACCCGTATTCAATTTCGC 57.194 40.909 0.00 0.00 0.00 4.70
2454 5450 3.246699 ACATACCCGTATTCAATTTCGCG 59.753 43.478 0.00 0.00 0.00 5.87
2455 5451 0.375803 ACCCGTATTCAATTTCGCGC 59.624 50.000 0.00 0.00 0.00 6.86
2456 5452 0.655733 CCCGTATTCAATTTCGCGCT 59.344 50.000 5.56 0.00 0.00 5.92
2457 5453 1.594518 CCCGTATTCAATTTCGCGCTG 60.595 52.381 5.56 0.00 0.00 5.18
2458 5454 1.104579 CGTATTCAATTTCGCGCTGC 58.895 50.000 5.56 0.00 0.00 5.25
2459 5455 1.528807 CGTATTCAATTTCGCGCTGCA 60.529 47.619 5.56 0.00 0.00 4.41
2460 5456 2.104144 GTATTCAATTTCGCGCTGCAG 58.896 47.619 10.11 10.11 0.00 4.41
2461 5457 0.799534 ATTCAATTTCGCGCTGCAGC 60.800 50.000 29.12 29.12 37.78 5.25
2462 5458 1.855213 TTCAATTTCGCGCTGCAGCT 61.855 50.000 34.22 13.71 39.32 4.24
2463 5459 1.443194 CAATTTCGCGCTGCAGCTT 60.443 52.632 34.22 18.97 39.32 3.74
2464 5460 1.005294 CAATTTCGCGCTGCAGCTTT 61.005 50.000 34.22 15.63 39.32 3.51
2465 5461 0.730494 AATTTCGCGCTGCAGCTTTC 60.730 50.000 34.22 21.69 39.32 2.62
2466 5462 2.839324 ATTTCGCGCTGCAGCTTTCG 62.839 55.000 34.22 30.30 39.32 3.46
2479 5475 4.629523 TTTCGCCGCCGAGGGTTT 62.630 61.111 0.00 0.00 45.35 3.27
2487 5483 2.983592 CCGAGGGTTTGCGGCTTT 60.984 61.111 0.00 0.00 41.17 3.51
2488 5484 2.255252 CGAGGGTTTGCGGCTTTG 59.745 61.111 0.00 0.00 0.00 2.77
2489 5485 2.258013 CGAGGGTTTGCGGCTTTGA 61.258 57.895 0.00 0.00 0.00 2.69
2490 5486 1.586154 CGAGGGTTTGCGGCTTTGAT 61.586 55.000 0.00 0.00 0.00 2.57
2491 5487 0.603065 GAGGGTTTGCGGCTTTGATT 59.397 50.000 0.00 0.00 0.00 2.57
2492 5488 0.318120 AGGGTTTGCGGCTTTGATTG 59.682 50.000 0.00 0.00 0.00 2.67
2493 5489 0.670239 GGGTTTGCGGCTTTGATTGG 60.670 55.000 0.00 0.00 0.00 3.16
2494 5490 1.291184 GGTTTGCGGCTTTGATTGGC 61.291 55.000 0.00 0.00 0.00 4.52
2495 5491 1.005156 TTTGCGGCTTTGATTGGCC 60.005 52.632 0.00 0.00 44.43 5.36
2496 5492 2.447586 TTTGCGGCTTTGATTGGCCC 62.448 55.000 0.00 0.00 45.01 5.80
2497 5493 4.496927 GCGGCTTTGATTGGCCCG 62.497 66.667 0.00 0.00 45.01 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1138 1157 5.893824 TGTAGATGCCTCTCTGAACTAATGA 59.106 40.000 0.00 0.00 32.66 2.57
2440 5436 2.104144 CTGCAGCGCGAAATTGAATAC 58.896 47.619 12.10 0.00 0.00 1.89
2443 5439 1.442520 GCTGCAGCGCGAAATTGAA 60.443 52.632 25.23 0.00 0.00 2.69
2462 5458 4.629523 AAACCCTCGGCGGCGAAA 62.630 61.111 33.90 14.28 0.00 3.46
2471 5467 1.586154 ATCAAAGCCGCAAACCCTCG 61.586 55.000 0.00 0.00 0.00 4.63
2472 5468 0.603065 AATCAAAGCCGCAAACCCTC 59.397 50.000 0.00 0.00 0.00 4.30
2473 5469 0.318120 CAATCAAAGCCGCAAACCCT 59.682 50.000 0.00 0.00 0.00 4.34
2474 5470 0.670239 CCAATCAAAGCCGCAAACCC 60.670 55.000 0.00 0.00 0.00 4.11
2475 5471 1.291184 GCCAATCAAAGCCGCAAACC 61.291 55.000 0.00 0.00 0.00 3.27
2476 5472 1.291184 GGCCAATCAAAGCCGCAAAC 61.291 55.000 0.00 0.00 39.87 2.93
2477 5473 1.005156 GGCCAATCAAAGCCGCAAA 60.005 52.632 0.00 0.00 39.87 3.68
2478 5474 2.656055 GGCCAATCAAAGCCGCAA 59.344 55.556 0.00 0.00 39.87 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.